With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers:

Programming basics and working with DNA sequences and strings

Debugging your code

Simulating gene mutations using random number generators

Regular expressions and finding motifs in data

Arrays, hashes, and relational databases

Regular expressions and restriction maps

Using Perl to parse PDB records, annotations in GenBank, and BLAST output

James Tisdall

James Tisdall has worked as a musician, a programmer at Bell Labs (where he programmed for speech research and discovered a formal language for musical rhythm), and as a bioinformaticist at Mercator Genetics in Menlo Park, California, and at Fox Chase Cancer Center in Philadelphia. He has a B.A. in mathematics from the City College of New York and an M.S. in computer science from Columbia University; he is working towards a Ph.D. in computer science at the University of Pennsylvania. In his spare time, Jim teaches computer music at the Settlement Music School in Philadelphia. He is also the author of O'Reilly's Beginning Perl for Bioinformatics.

Our look is the result of reader comments, our own experimentation, and feedback from distribution channels. Distinctive covers complement our distinctive approach to technical topics, breathing personality and life into potentially dry subjects. The animals on the cover of Beginning Perl for Bioinformatics are green frog (Rana clamitans) and American bullfrog (Rana catesbeiana) tadpoles.Tadpoles are the larvae of frogs and toads. They are aquatic and when first hatched have large, round heads and long, flat tails. Through a complex process of metamorphosis, tadpoles change from small fishlike creatures to the more familiar frogs and toads. This process can take from 10 days to 3 years depending on the species.During the first stages of metamorphosis, a tadpole's hind legs sprout, its head begins to flatten, and its tail becomes shorter. In its early life, a tadpole feeds primarily on diatoms, algae, and small quantities of zooplankton. As metamorphosis continues, it stops eating and begins to reabsorb its tail for sustenance while its digestive system changes from primarily vegetarian to carnivorous. During the final stages of metamorphosis, the tadpole's front legs appear, its jaws form, its skeleton hardens, and its gills disappear as the lungs develop. It soon begins to breathe air at the surface of the water. A short time later, the tadpole emerges from the water, reabsorbs the last of its tail, and hops off as a frog or a toad. Mary Anne Weeks Mayo was the production editor and copyeditor for Beginning Perl for Bioinformatics. Matt Hutchinson and Jane Ellin provided quality control. Edie Shapiro, Matt Hutchinson, and Derek DiMatteo provided production assistance. Ellen Troutman-Zaig wrote the index.Ellie Volckhausen designed the cover of this book, based on a series design by Edie Freedman. The cover image is an original illustration created by Lorrie LeJeune. Emma Colby produced the cover layout with Quark XPress 4.1 using Adobe's ITC Garamond font.Melanie Wang designed the interior layout, based on a series design by David Futato. Neil Walls converted the files from SGML to FrameMaker 5.5.6 using tools created by Mike Sierra. The text font is Linotype Birka; the heading font is Adobe Myriad Condensed; and the code font is LucasFont's TheSans Mono Condensed. The illustrations that appear in the book were produced by Robert Romano and Jessamyn Read using Macromedia FreeHand 9 and Adobe Photoshop 6. The tip and warning icons were drawn by Christopher Bing. This colophon was written by Lorrie LeJeune.

I used this book when I was a researcher in college and it helped a lot. Many of the examples in the book are directly applicable to work you will do in a lab. While this book does not have everything I found it an invaluable resource for anyone who is new to perl and bioinformatics in general.

This is good book, I ahvent read it all but its very comprehesive! I think that I'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank. Bye Kate Lea

This is good book, I ahvent read it all but its very comprehesive! I think that I'll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank. Bye Kate Lea

This is certainly a superb book. I really enjoyed it. Here are some of the advantages of "Beginning Perl for Bioinformatics" over other entry level general purpose Perl books such as "Learning Perl".

(1) Most importantly, you learn Perl in the context of dealing with biological problems (e.g., parsing BLAST output) rather than general problems that will not even remotly interest you (e.g., parsing employee's address list). So you will be kept interested throughout the book.

(2) Entire codes, rather than code snippets, are presented.

(3) Explanations are much more friendly and clear.

(4) You can find some useful materials that are not covered in Learning Perl; for example, using Perl debugger, using range operator to skip lines, etc.

One problem with this book is that there are TONS of errata (I'm referring to October 2001, 1st edition). Most of their corrections are available from the book website, and half of them are re-phrasing of sentences, so errata will not prevent you from understanding the book. But it certainly takes significant amount of time to go through the HUGE list of errata corrections (I also found more than ten additional errata that are not found in the errata list and reported to publisher). So if it's not urgent for you, wait until next reprint becomes available.

One more wish list is that Bioperl module could have been covered (It is briefly mentioned over seven pages but not actually covered). Hopefully, the upcoming book (June 2003) "Mastering perl for bioinformatics" will cover it.

This book is ok, not all that great for beginners. Has a lot of info, and the author shows you how to solve specific problems, but does not really show you how to deal with related problems. There are many errors, which is not unusual when people write books. The best way to learn perl is that you still have to learn the perl language itself to really understand it. This books has lots of examples, and if you happen to have the exact problems that you need to solve, then it is not bad. But to be honest with all you readers, the best way still is to read from other orielly's books on perl. And start programming from scratch! Goodluck to all ya!